Odd type of flash to h.264 conversion?

I have some (652 to be exact) flv videos that need to be converted to h.264 mp4 to play on devices running IOS. For some reasons while the other couple thousand videos converted fine in iSquint with these files in iSquint I get an error saying "VIDEO_TS folders can't be directly converted" its a standard flash video that works fine in quicktime and on a web based flash player but it refuses to convert. Since iSquint is no longer in development I can't contact the owner but does anyone know a solution to this? Handbrake works perfectly for converting these videos to mp4 and they play without problems but the problem with Handbrake is I can't just drop in the 652 files and hit go. I liked iSquint because I was able to just drop all the files in and press go. I don't want to sit here and drag and drop and wait on all videos for obvious reasons but this number of videos is way to large to just accept as unconvertible. Does anyone know of an app that supports drag and drop and will go beyond the limitations of iSquint? I have used ffmpeg to do these conversions but my server host has made it clear that if I try to convert hundreds of videos at once they will close my account also I don't want to find all the files in the folder that refuse to convert. I plan to just reconvert all the files again because sorting out the problem ones would take to long. So if anyone knows of a good (preferably free but I know that might not work) flv to h.264 converter that will allow me to specify about 2,000 files at once to convert I would really appreciate the info.

A simple script should be easy enough to write to figure out what has already been converted. You shouldn't even need that. Just ls in alphabetical order the flvs and the mp4s into separate temp files, strip the extensions and do a diff on the two temp files.

Automator might be useful for gathering a list of files and passing it to an program one by one. Can't say I've done that.

I don't understand why you would be getting that VIDEO_TS error for an flv file.

MPEG Streamclip can do batch conversions and I have used it plenty of times to convert .flvs to .movs or other formats and using different codecs.
Just make sure you have Perian installed, then open MPEG Streamclip, CMD+B to open Batch List, add your files, select an output directory and then your transcode/export settings and let it run through all the files.

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